Marius,
Thanks for this suggestion! John also suggested this on IRC. I had thought about this, but I initially avoided it for some technical reasons. However, I'm happy to say this is working for me. Thanks again for the pointers!
Phil
On Thu, Dec 1, 2016 at 11:33 AM, Marius van den Beek <m.vandenbeek@gmail.com
wrote:
I hope John can give some more input on this,
but if you're really short on time you could try the ssh runner
directly from galaxy without pulsar. I'm very happy with this driving a Torque 4 cluster.
The relevant part of my job_conf.xml looks like this:
<destination id="bicalc" runner="cli"> <param id="shell_plugin">SecureShell</param> <param id="job_plugin">Torque</param> <param id="shell_username">myusername</param> <param id="shell_hostname">submitnode.curie.fr</param> <param id="job_Resource_List">walltim e=2:00:00,nodes=1:ppn=8,mem=32gb</param> <param id="remote_metadata">true</param> <env file="/bioinfo/guests/mvandenb/galaxy/.venv/bin/activate" /> </destination>You'll only have to be able to do a passwordless ssh login using your galaxy user.
Best,
Marius
On 01/12/2016 15:35, Philip Blood wrote:
Hi Folks,
I'm working on a time-sensitive project (just a day or two left to sort it out) that requires I be able to submit jobs from a remote resource (TACC) to my resources (Pittsburgh Supercomputing Center) using a shared filesystem for data rather than staging via Pulsar. I've tried to set it up so that Pulsar does not do any staging, but is just handling the remote job submission and tool dependencies. However, Pulsar continues to use a local staging directory for the data and then copies the data back to the Galaxy directory.
What I'm hoping to do is have all the data stay in the shared filesystem for the entire course of the job. The quick test below does not have input data, but just issues commands on the remote compute node and generates output.
I'm using latest stable releases of Galaxy (16.07, installed on a TACC VM) and Pulsar (installed via pip at PSC). If anyone can provide some quick pointers I'd appreciate it.
Here are relevant parts of my configuration and some of the log output:
*Shared filesystem:* /hopper
*Local staging dir created by Pulsar:* /usr/local/packages/pu lsar/etc/files/staging
*galaxy.ini* file_path = /hopper/sy3l67p/blood/galaxy_home/database/files new_file_path = /hopper/sy3l67p/blood/galaxy_home/database/tmp job_working_directory = /hopper/sy3l67p/blood/galaxy_h ome/database/job_working_directory tool_dependency_dir = /hopper/sy3l67p/blood/galaxy_h ome/database/dependencies dependency_resolvers_config_file = /hopper/sy3l67p/blood/galaxy_h ome/config/dependency_resolvers_conf.xml
*job_conf.xml * <destination id="pulsar" runner="pulsar_rest"> <param id="url">https://128.182.99.126:8913/</param> <param id="default_file_action">none</param> <param id="file_action_config">/home/ tg455546/galaxy/config/file_actions.yaml</param> <param id="dependency_resolution">remote</param> <param id="submit_native_specification">-q batch</param>
</destination>*file_actions.yml* paths: # If Galaxy, the Pulsar, and the compute nodes all mount the same directory # staging can be disabled altogether for given paths.
- path: /hopper/sy3l67p/blood/galaxy_home/database/files action: none
- path: /hopper/sy3l67p/blood/galaxy_home/database/job_working_directory action: none
*app.yml*
manager: type: queued_drmaa dependency_resolvers_config_file: /usr/local/packages/pulsar/etc /dependency_resolvers_conf.xml tool_dependency_dir: /usr/local/packages/pulsar/dependencies
*Galaxy paster.log* galaxy.jobs DEBUG 2016-12-01 08:07:35,770 (50) Working directory for job is: /hopper/sy3l67p/blood/galaxy_home/database/job_working_directory\ /000/50 pulsar.client.staging.down INFO 2016-12-01 08:08:08,305 collecting output output with action FileAction[action_type=copy] pulsar.client.client DEBUG 2016-12-01 08:08:08,814 Copying path [/usr/local/packages/pulsar/etc/files/staging/50/working/output] to [/hopper/\ sy3l67p/blood/galaxy_home/database/files/000/dataset_50.dat]
*Pulsar uwsgi.log* 2016-12-01 09:07:38,174 INFO [pulsar.managers.base.base_dr maa][[manager=_default_]-[action=preprocess]-[job=50]] Submitting DRMA\ A job with nativeSpecification [-q batch] t #78bc [ 539.97] -> drmaa_allocate_job_template t #78bc [ 539.97] <- drmaa_allocate_job_template =0: jt=0x7f69cc002f80 t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80, name='drmaa_remote_command', value='/usr/local/packages/pulsar/etc/\ files/staging/50/command.sh') t #78bc [ 539.97] -> fsd_template_set_attr(drmaa_re mote_command=/usr/local/packages/pulsar/etc/files/staging/50/command.sh) t #78bc [ 539.97] <- drmaa_set_attribute =0 t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80, name='drmaa_output_path', value=':/usr/local/packages/pulsar/etc/fi\ les/staging/50/stdout') t #78bc [ 539.97] -> fsd_template_set_attr(drmaa_ou tput_path=:/usr/local/packages/pulsar/etc/files/staging/50/stdout) t #78bc [ 539.97] <- drmaa_set_attribute =0 t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80, name='drmaa_job_name', value='pulsar_50') t #78bc [ 539.97] -> fsd_template_set_attr(drmaa_job_name=pulsar_50) t #78bc [ 539.97] <- drmaa_set_attribute =0 t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80, name='drmaa_error_path', value=':/usr/local/packages/pulsar/etc/fil\ es/staging/50/stderr') t #78bc [ 539.97] -> fsd_template_set_attr(drmaa_er ror_path=:/usr/local/packages/pulsar/etc/files/staging/50/stderr) t #78bc [ 539.97] -> drmaa_set_attribute(jt=0x7f69cc002f80, name='drmaa_native_specification', value='-q batch') t #78bc [ 539.97] -> fsd_template_set_attr(drmaa_native_specification=-q batch) t #78bc [ 539.97] <- drmaa_set_attribute =0 t #78bc [ 539.97] -> drmaa_run_job(jt=0x7f69cc002f80) t #78bc [ 539.97] -> pbsdrmaa_session_run_impl(jt=0x7f69cc002f80, bulk_idx=-1) t #78bc [ 539.97] -> fsd_template_set_attr(Checkpoint=u) t #78bc [ 539.97] -> fsd_template_set_attr(Keep_Files=n) t #78bc [ 539.97] -> fsd_template_set_attr(Priority=0) t #78bc [ 539.97] -> pbsdrmaa_write_tmpfile t #78bc [ 539.97] <- pbsdrmaa_write_tmpfile=/tmp/pbs_drmaa.n6VpuR t #78bc [ 539.97] -> fsd_template_set_attr(Job_Name=pulsar_50) t #78bc [ 539.97] -> fsd_template_set_attr(Output_P ath=/usr/local/packages/pulsar/etc/files/staging/50/stdout) t #78bc [ 539.97] -> fsd_template_set_attr(Error_Pa th=/usr/local/packages/pulsar/etc/files/staging/50/stderr) t #78bc [ 539.97] -> fsd_template_set_attr(Variable _List=PBS_O_WORKDIR=/usr/local/packages/pulsar/etc) t #78bc [ 539.97] -> pbsdrmaa_submit_apply_native_s pecification({native_specification=(null)}) d #78bc [ 539.97] * self->destination_queue = batch t #78bc [ 539.97] -> fsd_template_set_attr(submit_args=-q batch) d #78bc [ 539.97] * set attr: submit_args = -q batch d #78bc [ 539.97] * set attr: Job_Name = pulsar_50 d #78bc [ 539.97] * set attr: Variable_List = PBS_O_WORKDIR=/usr/local/packages/pulsar/etc d #78bc [ 539.97] * set attr: Priority = 0 d #78bc [ 539.97] * set attr: Output_Path = /usr/local/packages/pulsar/etc/files/staging/50/stdout d #78bc [ 539.97] * set attr: Keep_Files = n d #78bc [ 539.97] * set attr: Error_Path = /usr/local/packages/pulsar/etc/files/staging/50/stderr d #78bc [ 539.97] * set attr: Checkpoint = u
2016-12-01 09:08:06,707 INFO [pulsar.client.staging.down][ [manager=_default_]-[action=postprocess]-[job=50]] collecting output o\ utput with action FileAction[action_type=copy] 2016-12-01 09:08:06,708 INFO [pulsar.managers.stateful][[m anager=_default_]-[action=postprocess]-[job=50]] Status of job [50] ch\ anged to [complete]. No callbacks enabled.
-- Philip D. Blood, Ph.D. Senior Computational Scientist Voice: (412) 268-9329 Pittsburgh Supercomputing Center Fax: (412) 268-5832 Carnegie Mellon University Email: blood@psc.edu
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